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All Journal Indonesian Journal of Science and Technology Sang Pencerah: Jurnal Ilmiah Universitas Muhammadiyah Buton INDONESIAN JOURNAL OF MEDICAL LABORATORY SCIENCE AND TECHNOLOGY Journal of Applied Geology
Endah Retnaningrum
Universitas Gadjah Mada
Humanities Civil Engineering, Building, Construction & Architecture Computer Science & IT Earth & Planetary Sciences Education Energy Engineering Environmental Science Health Professions Social Sciences Other

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Preliminary Study of Liquid Hydrocarbon Biodegradation By Indigineous Bacteria Isolated from Wonocolo Village, Bojonegoro District, East Java Province Wahyu Wilopo; Bramono Dwi Kusumo; Endah Retnaningrum
Journal of Applied Geology Vol 2, No 2 (2017)
Publisher : Geological Engineering Department Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (458.91 KB) | DOI: 10.22146/jag.40862

Abstract

Aquatic environmental pollution due to petroleum waste can cause disruption to the environment and damaging of flora and fauna. It has been reported that petroleum contaminatin occurs in the Bengawan Solo river, East Java Province. Liquid hydrocarbon waste pollution can be remediate through various processes, one of them is biodegradation. Biodegradation a part of bioremediation, is the process by which organic substances are decomposed by microorganisms into simpler substances such as carbon dioxide, water and ammonia. Bioremediation has minor side effects compare to other methods because it’s more effective, efficient, economical and eco-friendly through biological process. This study aims to identify bacteria for liquid hydrocarbon degradation from the rivers in Wonocolo Village, Bojonegoro District and to determine maximum percentage of inoculum to produce the highest efficiency of liquid hydrocarbons degradation. Based on phenotypic characters, the selected bacteria was identified as a genus of Moraxella. Its bacterium with a concentration of 2 % can reduce hydrocarbons to a maximum of 0.67 % per hour at the exponential phase growth.
Lactobacillus Composed Urinary Microbiome of Healthy People and Urinary Tract Infection Patients Fitri Nadifah; Wayan Tunas Artama; Budi Setiadi Daryono; Endah Retnaningrum
Sang Pencerah: Jurnal Ilmiah Universitas Muhammadiyah Buton Vol 8 No 4 (2022): Sang Pencerah: Jurnal Ilmiah Universitas Muhammadiyah Buton
Publisher : Lembaga Penelitian dan Pengabdian Masyarakat Universitas Muhammadiyah Buton

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (328.812 KB) | DOI: 10.35326/pencerah.v8i4.2196

Abstract

Lactobacillus has long been known to reconstruct the microbiome of the urogenital organs of healthy people. However, changes in lactobacillus abundance are known occurring in urogenital tract infections (UTI) patients. It is also known that there are Lactobacillus species that have specific genomic characteristics and nutritional requirements that cause them to turn into pathogens. Understanding population characteristics and taxa composition that reconstruct urine microbiome is very important for the diagnosis and treatment of urogenital infections. This review provides an update information of metagenomic sequencing to identify the urinary microbiome profile and the role of lactobacilli in healthy and UTI patients.
Literature Review and Experiment: Diversity of Bacteria in Forest, Revegetated Post-Mining Land, and Active Tin Mining with A Metagenomic Approach Eka Sari; Andhika Puspito Nugroho; Endah Retnaningrum; Irfan Dwidya Prijambada
Indonesian Journal of Science and Technology Vol 8, No 1 (2023): IJOST: April 2023
Publisher : Universitas Pendidikan Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.17509/ijost.v8i1.51662

Abstract

The objective of this study was to investigate the diversity of bacteria in the rhizosphere of Acacia grow in the forest and different ages of revegetated land and non-rhizospheric bacteria from active tin mining soil on Bangka Island with a metagenomic approach and to investigate its relationship with physicochemical properties of the soil and its metal content. 17 species/genera were found in the four fields, and Bradyrhizobium is the dominant genus. Bacterial communities of the forest (more than 5 years in revegetated post-tin mining land containing C, N, P, and Fe) are Paraburkholderia sp., Bacillus sp., Candidatus-Xiphinematobacter, and Bacterium enrichment. The physicochemical properties of soil from less than 5 years of revegetated contain Cu, Cr, and Mo, and the dominant species in this soil were Bulkhorderia sp., Bacillus lehensis, B. fordii, B. thermolactis, Chloroflexi bacterium, and Thermonosporaceae bacterium. The physicochemical properties of soil from the mining were dominated by Cd and Ni, and the dominant species in this soil were Sinomonas atrocyanea.
Computational modeling of a Novel CTX-M β-lactamase Escherichia coliisolated from Yogyakarta, Indonesia Using I-TASSER and SWISS-MODEL Anggiresti Kinasih; Endah Retnaningrum
JURNAL INDONESIA DARI ILMU LABORATORIUM MEDIS DAN TEKNOLOGI Vol 8 No 1 (2026): Integration of Molecular Approaches in Addressing Drug Resistance and Changing Gl
Publisher : Universitas Nahdlatul Ulama Surabaya

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.33086/ijmlst.v8i1.7267

Abstract

Extended-spectrum β-lactamases (ESBLs), especially those of the CTX-M family, significantly contribute to antibiotic resistance in Escherichia coli. While CTX-M variants are well-characterized in clinical settings, their structural features in foodborne E. coli remain underexplored, particularly in countries like Indonesia. This study aimed to predict and validate the three-dimensional (3D) structure of a novel CTX-M β-lactamase protein from an E. coli isolate (D4DU2-ESBL-EC) culture collection at Laboratory of Microbiology, Universitas Gadjah Mada (UGM). This study reports a novel CTX-M variant from E. coli D4DU2, a locally strain originated from raw chicken meat in Yogyakarta traditional market that has been shown to adapt and thrive in Sleman Regency, Indonesia. Based on phylogenetic and structural analyses, E. coli D4DU2 evolutionary link to Indian CTX-M-15, with distinct mutations at W253L, P254A amino acid near the active site. The 3D structure of D4DU2 CTX-M β-lactamase was predicted using I-TASSER and validated using PROCHECK. Ramachandran analysis showed 78.4% of residues in the most favored regions, 20.5% in allowed regions, and only 1.2% in disallowed regions, confirming high stereochemical quality. These findings highlight potential local adaptation and emergence of a unique ESBL-producing E. coli strain. This study provides a reliable model for CTX-M β-lactamase from foodborne E. coli in Indonesia, supporting One Health-based surveillance and intervention strategies. Overall, this study demonstrates that I-TASSER, complemented by PROCHECK validation, offers a valuable in silico approach for the structural characterization of ESBL proteins from foodborne bacterial isolates in resource-limited contexts
Molecular approach to the characterization of lipase encoding genes from Moraxella sp. SBE01 Siti Soleha; Syarifah Syarifah; Tito Nurseha; Awalul Fatiqin; Endah Retnaningrum; Yitro Serang
JURNAL INDONESIA DARI ILMU LABORATORIUM MEDIS DAN TEKNOLOGI Vol 6 No 2 (2024): Promising and Valuable Research Towards Diagnosis, Prognosis and Treatment of Dis
Publisher : Universitas Nahdlatul Ulama Surabaya

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.33086/ijmlst.v6i2.5596

Abstract

Lipase from Moraxella sp. SBE01 is an expression of the gene encoding lipase. Detection and characterization of the Moraxella sp. SBE01 lipase coding gene is necessary for large-scale lipase production through genetic engineering. This study aimed to observe the molecular weight, amino acid sequence, length, and conserved amino acids in the DNA encoding the lipase gene, with the goal of identifying and characterizing the lipase-coding gene from Moraxella sp. SBE01. The primer design process was conducted to amplify the lipase gene from Moraxella sp. SBE01 using specialized software for sequence alignment and phylogenetic analysis. Amplification was carried out using PCR with the designed primer, forward primer (GTC ATG ATG TAC TTC CAY GGN GGN GG), reverse primer (GGT TGC CGC CGG CDS WRT CNC C). PCR was carried out under pre-denatured conditions at 95°C (3 minutes), followed by 30 cycles of denaturation at 95°C, annealing at 66°C (30 seconds), 70°C elongations (1 minute) and final elongation of 70°C (10 minutes). The PCR results were electrophoresed using 1% agarose gel with a 1 kb DNA marker. The PCR results were sequenced and analyzed for gene and amino acid sequences and the type of lipase expressed. Sequencing resulted in 387 bp of the nucleotide sequence. The gene and amino acid sequences from Moraxella sp. SBE01 had high homology with the gene and amino acid sequences from Moraxella sp. strain TA144. The lipase gene encodes a protein consisting of 129 amino acids and contains a conserved HGG (His-Gly-Gly) motif, which is characteristic of lipases in family IV, also known as the hormone-sensitive lipase (HSL) family. This conserved sequence suggests that the lipase shares structural and functional similarities with other enzymes in the HSL family, playing a key role in lipid metabolism.
Co-Authors Anggiresti Kinasih Bramono Dwi Kusumo BUDI SETIADI DARYONO Eka Sari Fatiqin, Awalul Fitri Nadifah Irfan Dwidya Prijambada Nugroho, Andika Puspito Siti Soleha Syarifah Syarifah Tito Nurseha Wahyu Wilopo Wayan Tunas Artama Yitro Serang